Because of their capacity to base pair, oligonucleotides are used widely as diagnostic reagents and as tools in molecular genetics. More recently "antisense" oligonucleotides have been shown to block the translation and perhaps transcription of genes and are now actively investigated as a new class of pharmaceuticals.
A number of alternative phosphate-containing linkages are known to exist in the literature. A great deal of effort has been directed toward the synthesis of oligonucleotide analogues with an altered phosphodiester linkage to improve cellular uptake and to decrease the rate of degradation of oligonucleotides by nucleases which cleave the phosphodiester linkage. Thus far, the most extensively studied analogues have contained modified phosphate linkages. These analogues include oligonucleotide alkylphosphotriesters, oligonucleotide methylphosphonates, oligonucleotidephosphorothioatesand oligonucleotide alkylphosphoramidates. In most of these compounds, the linkage consists of a pair of diastereoisomers which have not been separated. Consequently, an oligomer having n non-ionic internucleotide linkages will consist of a mixture of 2.sup.n isomers.
Other approaches to altering the backbone of oligonucleotides which are capable of forming a duplex or triplex include modifying the backbone. In these approaches the bridging phosphate group is replaced with other functional groups including carbonate, oxyacetamide, carbamate, silyl and ribonucleoside derived morpholino subunits linked by carbamate groups. However, these phosphate-free backbones are relatively instable with respect to hydrolysis, are relatively insoluble in water and form duplexes which appear to differ from that of the natural oligonucleotides. All of the above phosphate analogues and non-phosphate derivatives have a variety of problems in terms of uptake into the cell, attack by or lack of attack by nucleases, insolubility in aqueous solution, binding and relative stability of binding for duplex and triplex formation. The present invention provides an improved method to synthesize chemical compounds capable of forming double helix or triplex-forming oligonucleotides. These chemical compounds exhibit chemical characteristics necessary to form a duplex or triplex, yet replace the phosphodiester linkage of the oligonucleotide backbone. The present invention provides a novel class of compounds capable of entering the cell, resisting nuclease attack and forming stable triplex structures.